Module 1B - Biomolecules and Enzymes Flashcards
(205 cards)
1
Q
What is the shape and structure of proteins
A
structurally complex and
functionally sophisticated
molecules
2
Q
The Shape of a Protein Is Specified by Its ____ ___Sequence
A
Amino Acid
3
Q
How many types of amino acids in proteins
A
20 amino acids
4
Q
Proteins are made of long ____ ___of amino acids
A
unbranched chain
5
Q
Proteins are also known as?
A
polypeptides
6
Q
-repeating sequence of atoms along the core of the polypeptide chains
A
polypeptide backbone
7
Q
give amino acids its unique properties
A
Side chains
8
Q
Polar amino acids
A
Aspartic acid (Asp)
Glutamic acid (Glu)
Arginine (Arg)
Lysine (Lys)
Histidine (His)
Asparagine (Asn)
Glutamine (Gln)
Serine (Ser)
Threonine (Thr)
Tyrosine (Tyr)
9
Q
Non-polar amino acids
A
alanine (Ala)
Glycine (Gly)
Valine (Val)
Leucine (Leu)
Isoleucine (Ile)
Proline (Pro)
Phenylalanine (Phe)
Methionine (Met)
Tryptophan (Trp)
Cysteine (Cys)
10
Q
2 polar amino acids that have negative side chain
A
Aspartic acid and Glutamic acid
11
Q
3 polar amino acids that have positive side chain
A
Arginine
Lysine
Histidine
12
Q
5 polar amino acid that has uncharged polar
A
Asparagine
Glutamine
Serine
Threonine
Tyrosine
13
Q
Has weak noncovalent bonds
A
Protein folding
14
Q
3 weak noncovalent bonds
A
- hydrogen bonds
-electrostatic attractions
-van der Waals
15
Q
hydrophobic molecules, including the nonpolar side chains of amino acids, tend to be forced together in an aqueous environment to minimize their disruptive effect on the hydrogen bonded network of water
A
hydrophobic clustering forces
16
Q
_____ ____, including the _____ ___ ___tend to be forced together in an aqueous environment to minimize their disruptive
effect on the hydrogen-bonded network of water molecules
A
hydrophobic molecules, including the nonpolar side chains of amino acids
17
Q
In the folded confirmation in aqueous environment of protein, it can form hydrogen bonds to water
A
Polar side chain on the outside of the molecule
18
Q
the folded confirmation in aqueous environment of protein has hydrophobic core region which contains _____ __ __
A
nonpolar side chains
19
Q
an important factor governing the folding of any protein is the distribution of its ___ and ___ ___
A
hydrophobic (nonpolar) and polar groups
20
Q
determined by the order of the amino acids in its chain
A
three-dimensional structure of protein
21
Q
reversible changes in a protein’s structure
A
denatures ↔ renatures
22
Q
contain all the information needed for specifying the three-dimensional shape of a protein
A
Amino acids
23
Q
A protein can be unfolded, or ____, by treatment with certain solvents, which disrupt the noncovalent interactions holding the folded chain together. This treatment converts the protein into a flexible polypeptide chain that has lost its natural shape
A
denatured
24
Q
When the denaturing solvent is removed, the protein often refolds spontaneously, or _____, into its original conformation, indicating that all the information needed for specifying the three-dimensional shape of a protein is contained in its amino acid sequence.
A
renatures
25
Assist in the protein folding
Molecular chaperones
26
2 regular folding patterns
The α Helix and the β sheet
27
α helix and β sheet are particularly common because they result from hydrogen-bonding between ___-__ and __=__ in the polypeptide group
N-H and C=O groups
28
- The first folding pattern to be discovered
- was found in the protein α-keratin, which is abundant in skin and its derivatives—such as hair, nails, and horns.
α helix
29
found in the protein fibroin, the major constituent of silk.
β sheet
30
β sheets can form either from ____ ___ or ______ __
parallel chains or antiparallel chains
31
form from neighboring segments of the polypeptide backbone that run in the same orientation
Parallel chains
32
from a polypeptide backbone that folds
back and forth upon itself, with each section of the chain running in the direction opposite of that of its immediate neighbors
antiparallel chains
33
generated when a single
polypeptide chain twists around on itself to form a rigid cylinder
a helix
34
A hydrogen bond is made between every ___ peptide – linking C=O of one peptide bond to N-H of another
4th
35
wrap around each other to form a particularly stable structure, known as a coiled-coil.
α helices
36
formed from two or more have most of their nonpolar (hydrophobic)
side chains on one side
coiled-coil
37
Modular units from
which larger proteins are built
Protein domains
38
- a substructure produced by any part of a polypeptide chain that can fold independently into a compact, stable structure
-contains between 40 and 350 amino acids
Protein domains
39
four levels of organization in the structure of a protein
1. Primary structure
2. Secondary structure
3. Tertiary structure
4. Quaternary structure
40
Primary structure of protein
Amino acid sequence
41
Secondary structure of protein
hydrogen bonding of the peptide backbone; helices and β sheets
42
tertiary structure of protein
full 3D organization of a polypeptide chain
43
Quaternary structure of protein
protein molecule formed as a complex of more than one polypeptide chain
44
many present-day
proteins can be grouped
into protein ____
families
45
each protein family member has an ___ ___ ___ and a __-____conformation that resemble those of the other family members.
amino acid sequence and a three-dimensional conformation
46
a large family of protein-cleaving (proteolytic) enzymes that includes the digestive enzymes chymotrypsin, trypsin, and elastase, and several proteases involved in blood clotting
serine proteases
47
has been more highly conserved than the amino acid sequence
the structure of the
different members of a
protein family
48
- both gene regulatory proteins in the homeodomain family4
- identical in only 17 of 60 aa residues
yeast α2 protein and the
Drosophila engrailed
protein
49
protein families are readily recognized when the ___ of any organism is
sequenced
genome
50
human genome = ____ protein-coding genes
21,000
51
40% of our protein-coding genes to known protein structures, ___ diff
families
500
52
are the most powerful and predominant techniques used to experimentally determine the three-dimensional structures of biological macromolecules at near atomic resolution
x-ray crystallography and nuclear
magnetic resonance (NMR)
53
the basic units of proteins that can fold, function, and evolve independently
Protein domains
54
process of creating new combination of gene functional domains
Domain shuffling
55
– subset of protein domains, mobile
during evolution
protein modules
56
The three-dimensional structures of some protein modules
1. Immunoglobulin module
2. Fibronectin type 3 module
3. Kringle module
57
easily integrated into other proteins
Protein domains
58
can be readily linked in
series to form extended
structures
Domains
59
Major Histocompatibility Complex (MHC) has ____-___ ___ that bind to and present fragments of pathogens (antigens) to immune cells.
antigen-recognition domain (only in humans)
60
Human genome encodes
how many protein-coding genes
21,000 protein-coding genes
61
genome sequences also reveal that _____
have inherited
nearly all of their protein
domains from invertebrates with only 7% identified human domains being vertebrate-specifics
Vertebrate
62
has given rise to many novel combinations of protein domains
domain shuffling during
vertebrate evolution
63
allow proteins to bind to each other to produce
structures in the cell
weak noncovalent bonds
64
any region of a protein’s
surface that can interact with another
molecule
binding site
65
forming a symmetric complex of two protein
subunits (dimer)
"head-to-head” arrangement
66
Contains two identical α-globin subunits and two identical β-globin subunits, symmetrically arranged
hemoglobin
67
a long chain of identical
protein molecules can be
constructed if each molecular
has a ___ __
complementary to another
region of the surface of the
same molecule
binding site
68
long helical structure produced from many
molecules of the protein actin
actin filament
69
why is a helix a common
structure in biology?
all subunits are identical, they can only fit together in one way – rarely straight line –resulting in a helix (resembles
a staircase
70
Elongated, fibrous shapes protein molecules
-fibrous protein
- keratin filaments
- a-keratin
- intermediate filaments
71
elongated three-dimensional
structure
Fibrous protein
72
main component in long
lived structures
Keratin filaments
73
a dimer of two identical subunits
a-keratin
74
rope-like structures; important component of the cytoskeleto
intermediate filaments
75
- abundant outside the cell
- main component of the
gel-like extracellular
matrix
Fibrous protein
76
consists of three long polypeptide chains,
each containing
that nonpolar
amino acid glycine
at every 3rd position
collagen
77
collagen consists
of three long
polypeptide chains,
each containing
that nonpolar
amino acid ____
at every ___ position
glycine
3rd
78
another abundant
protein in ecm; highly
disordered polypeptide
elastin
79
Ep1 PHD PHD Ep2
Yeast
80
Ep1 PHD PHD Ep2 Br
Worm
81
Znf Ep1 PHD PHD Ep2 Br BMB
Human
82
Elastin molecules are formed from relatively ___ and ___ polypeptide chains that are covalently cross-linked into a rubberlike elastic meshwork
loose and unstructured
83
The loose and unstructured chains that forms elastin molecules are covalently cross-linked into a rubberlike ____ ____
elastic meshwork
84
intrinsically disordered regions of
proteins are frequent in nature,
WHY?
to form specific binding sites for other protein molecules that are of high specificity
85
What does intrinsically disordered regions of
proteins trigger?
cell signaling events
86
intrinsically disordered regions of
proteins serve as a ____, to hold two
protein domains in close
proximity
tether
87
intrinsically disordered regions of proteins create regions with ___ _____
restrict diffusion
88
proteins secreted
extracellular are often
stabilized by ____ ___ ____
covalent
cross-linkages
89
The most common cross-linkages in proteins
sulfur–sulfur bonds- disulfide bonds (also called S–S bonds)
90
do not change the conformation of a protein but instead act as atomic staples to reinforce its most favored conformation
disulfide bonds
91
disulfide bonds act as ____ ____
atomic
staples
92
3 advantages of using smaller subunits to build larger structures
1. requires only a small amount of genetic information
2. Both assembly and disassembly can be readily controlled, because the subunits associate through multiple bonds of relatively low energy.
3. Errors in the synthesis of the structure can be more easily avoided
93
some form into ____ and
____ that bind specific
RNA and DNA molecules in
their interior.
- the formation of closed structures provides additional stability because it increases the number of bonds between the protein subunits
tubes and spheres
94
made of hundreds of identical
protein subunits that enclose
and protect the viral nucleic
acid
protein coat or capsid of
viruses
95
_____ _____ can spontaneously assemble into the final structure under the appropriate conditions.
purified subunits
96
first large macromolecular aggregate shown to be capable of self-assembly from its component parts
tobacco mosaic virus (TMV)
97
Not all cellular structures held together by noncovalent bonds are capable of ____-_____
self-assembly
98
guide
construction but take no part in
the final assembled structure
assembly factors
99
self-propagating, stable β-sheet
aggregates
amyloid fibrils
100
may be
released from dead cells and
accumulate as amyloid
protein aggregates
101
protein aggregates may be released from dead cells and accumulate as
amyloid
102
can kill cells and damage
tissues
Amyloid
103
most severe amyloid pathologies
neurodegenerative diseases
(Alzheimer’s & Parkinson’s)
104
group of disorders caused by a specific type of misfolded protein called the prion protein (PrP)
Prion diseases
105
Example of prion disease in sheep
- scrapie
106
Example of prion disease in humans
- Creutzfeldt-Jakob disease (CJD)
- Kuru in humans
107
Example of prion disease in cattles
bovine
spongiform encephalopathy (BSE)
108
Prion disease is caused by a misfolded, aggregate
form of a particular protein called ____
PrP
(prion protein)
109
PrP
(prion protein) can form ____ ___ that are “infectious”
amyloid fibrils
110
- acts like a vesicle containing peptide
and hormones
- in bacteria, secretes proteins
that form long amyloid fibrils
projecting from the cell
exterior that help to bind
bacterial neighbors to biofilms
specialized “secretory
granules” that consist of
amyloid fibrils
111
a protein molecule’s
physical interaction with
other molecules determines
its ___ ___
biological properties
112
each protein
molecule can usually bind
just one or a few molecules
out of many thousands
specificity
113
the substance that
is bound by the protein
ligand
114
The ability of a
protein to bind
selectively and with
high affinity to a
ligand depends on
the formation of a set
of ___ ___ bonds
weak noncovalent
bonds
115
the region
of protein that associates
with a ligand
binding site
116
their interaction may
restrict the access of water molecules to that protein’s ligand-binding sites
neighboring parts of the polypeptide chain
117
can alter
their reactivity
the clustering of neighboring polar amino acid chains
118
Proteins bind to other proteins through three types of interfaces, namely:
- surface-string interaction
- helix-helix
- surface-surface
119
binds tightly to a particular
target molecule (antigen),
inactivating directly or
making it for destruction
antibody or
immunoglobulins
120
Where does antibody or
immunoglobulins binds to
target molecule (antigen)
121
2 purposes of the binding of an antibody to its antigen
Direct inactivation or
making it for destruction
122
Antibodies are typically ____shaped molecules
Y-shaped
123
The arms of the Y-shaped molecules form two identical ___ ___ that are complementary to
a small portion of the
surface of the ____
molecule
binding sites
antigen
124
- cause the chemical
transformations that
make and break
covalent bonds in cells
- speed up reactions,
act as catalysts
enzymes
125
_____ + ___→ products
enzymes + substrates
126
Michaelis-Menten mechanism or the enzyme-substrate complex reaction pathway
E + S → ES → EP → E + P
127
there is a limit to the amount of
_____ that a single enzyme
molecule can process in a
given time
substrate
128
the
maximum rate of reaction
divided by the enzyme
concentration
turnover number
129
What do enzymes achieve?
enzymes achieve extremely high
rates of chemical reactions
130
Where do enzymes greatly increases the
local concentration of both these
substrate molecule
catalytic
site
131
unstable
intermediate state
transition state
132
the free
energy required to attain the
transition state
activation energy
133
enzymes not only bind tightly
to a transition state, they also
contain precisely ____ ___
positioned
atoms
134
What do precisely positioned atoms do?
alter the electron
distributions in the atoms that
participate directly in the
making and breaking of
covalent bonds
135
adds a molecule of water to a single bond
between two adjacent sugar groups in the polysaccharide chain, thereby causing the bond to
break
hydrolysis
136
enzymes have a ____ ___ or ___ ___ tightly associated
with their active site that assists with their catalytic funciton
small molecule or metal atom
137
General term for enzymes that catalyze a hydrolytic cleavage reaction
Hydrolases
138
What are the more specific names for subclasses of hydrolases
Nucleases and proteases
139
- Break down nucleic acids by hydrolyzing bonds between nucleotides.
- Endo- and exonucleases cleave nucleic acids within and from the ends of the polynucleotide chains, respectively
Nucleases
140
Break down proteins by hydrolyzing bonds between amino acids
Proteases
141
Synthesize molecules in anabolic reactions by condensing two smaller molecules together
Synthases
142
-Join together (ligate) two molecules in an energy - dependent process.
Ligases
143
Joins two DNA molecules together end-to-end through phosphodiester bonds
DNA ligase
144
Catalyze the rearrangement of bonds within a single molecule
Isomerase
145
Catalyze polymerization reactions such as the synthesis of DNA and RNA
polymerases
146
Catalyze the addition of phosphate groups to molecules.
Kinases
147
Important group of kinases that attach the phosphate groups to protein
Protein kinases
148
Catalyze the hydrolytic removal of a phosphate group from a molecule
Phosphatases
149
General name for enzymes that catalyze reactions in which one molecule is oxidized while the other is reduced
Oxido-Reductases
150
Oxido-Reductases are often more specifically names as?
Oxidases , reductases, or dehydrogenase
151
-hydrolyze ATP
- Many proteins with a wide range of roles have an energy-harnessing ___ activity as part of their function; for example, myosin and sodium-potassium pump
ATPases
152
-Hydrolyze GTP
- A large family of GTP-binding proteins, with central roles in the regulation of cell processes
GTPases
153
Enzymes that were discovered and named before the convention became generally accepted at the end of 19th cent.
pepsin, trypsin, thrombin, lysozyme
154
Coenzyme of thiamine (vitamin B1)
Thiamine pyrophosphate
155
Enzyme-catalyzed reactions requiring the coenzyme thiamine pyrophosphate
Activation and transfer of aldehydes
156
Coenzyme of Riboflavin (vitamin B2)
FADH
157
Enzyme-catalyzed reactions requiring the coenzyme FADH
Oxidation-reduction
158
Coenzyme of Niacin
NADH, NADPH
159
Enzyme-catalyzed reactions requiring the coenzyme NADH, NADPH
Oxidation-reduction
160
Coenzyme of pantothenic acid
Coenzyme A
161
Enzyme-catalyzed reactions requiring the coenzyme A
Acyl group activation and transfer
162
Coenzyme of pyridoxine
Pyridoxal phosphate
163
Enzyme-catalyzed reactions requiring the coenzyme pyridoxal phosphate
Amino acid activation; also glycogen phosphorylase
164
Coenzyme of biotin
Biotin
165
Enzyme-catalyzed reactions requiring the coenzyme biotin
CO2 activation and transfer
166
Coenzyme of lipoic acid
Lipoamide
167
Enzyme-catalyzed reactions requiring the coenzyme lipoamide
Acyl group activation; oxidation-reduction
168
Coenzyme of folic acid
Tetrahydrofolate
169
Enzyme-catalyzed reactions requiring the coenzyme tetrahydrofolate
Activation and transfer of single carbon groups
170
Coenzyme of Vitamin B12
Cobalamin coenzyme
171
Enzyme-catalyzed reactions requiring the coenzyme cobalamin coenzyme
Isomerization and methyl group transfers
172
other proteins also frequently
require specific ___ ___ adjuncts to
function properly
small molecule
173
- receptor protein in the eye involved in vision
- produced when light enters retina
rhodopsin
174
a small molecule derived from vitamin A, binds tightly to rhodopsin and enables it to detect light, which is essential for vision
Retinal
175
a protein in red blood cells that carries oxygen
hemoglobin
176
a small iron-containing molecule, binds tightly to hemoglobin and allows it to capture and release oxygen molecules effectively.
heme
group
177
a
large protein assembly;
allows the product of enzyme
A to be passed directly to
enzyme B, and so on
multienzyme complex
178
controls how many
molecules of each enzyme
it makes by regulating the
expression of the gene that
encodes that enzyme
Cells
179
How do cells control the number of enzyme molecules they produce
by regulating the
expression of the gene that
encodes that enzyme
180
How does the cell controls enzymatic
activities
by confining sets
of enzymes to particular
compartments
181
a
product produced late in a
reaction pathways inhibits
an enzyme that acts earlier
in the pathway
feedback inhibition
182
prevent an enzyme from
acting
negative regulation
183
regulatory molecule
stimulates the enzyme’s
activity rather than shutting
the enzyme down
positive regulation
184
Greek words meaning
“other”
allos
185
Greek words meaning
“solid” or “3D”
stereo
186
have at least
two binding sites on their surface –
an active site and a regulatory site
allosteric enzymes
187
recognizes the
substrates
active site
188
recognizes a regulatory
molecule
regulatory site
189
interaction between separated
sites on a protein
conformational change
190
can occur in
multimeric proteins, where
each subunit of the protein
has its own ligand-binding
site
cooperative allosteric
transition
191
Where does cooperative allosteric transition occur
multimeric proteins
192
transfer
of the terminal phosphate group
of an ATP molecule to the
hydroxyl group
protein phosphorylation
193
phosphorylates
protein kinase
194
phosphate removal,
dephosphorylate
protein phosphatases
195
phosphate is part of guanine
nucleotide GTP; addition and
removal of phosphate
GTP-binding proteins
196
the loss of a phosphate
group occurs when?
the
bound GTP is hydrolyzed to
GDP in a reaction catalyzed
by the protein itself, and in its
GDP-bound state the protein
is inactive
197
generate forces responsible for
muscle contraction and the crawling and
swimming of cells
motor proteins
198
Undergo a series of conformational changes; these
changes are reversible
motor proteins
199
coupling one of the
conformational changes to the
hydrolysis of an ATP molecule that is
tightly bound to the protein
unidirectional conformation
changes
200
function to export
hydrophobic molecules from the cytoplasm
ABC transporters (ATP-binding
cassette)
201
overproduction of these proteins
contributes to the resistance of
tumor cells to chemo
ABC transporters (ATP-binding
cassette)
202
each of the central processes in a
cell—such as DNA replication,
protein synthesis, vesicle budding,
or transmembrane signaling—is
catalyzed by a highly coordinated,
linked set of how many proteins
10 or more proteins (protein machines)
203
proteins binding sites
for multiple other
proteins
scaffold proteins
204
scaffold proteins serve both to:
1. link together
specific sets of interacting
proteins, and
2. to position them at
specific locations inside a cell
205
